4dkw: Difference between revisions

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 ==Structure of P22 Large terminase nuclease domain==
-<StructureSection load='4dkw' size='340' side='right' caption='[[4dkw]], [[Resolution|resolution]] 2.02&Aring;' scene=''>
+<StructureSection load='4dkw' size='340' side='right'caption='[[4dkw]], [[Resolution|resolution]] 2.02&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4dkw]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Bpp22 Bpp22]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DKW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4DKW FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4dkw]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Salmonella_virus_P22 Salmonella virus P22]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DKW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4DKW FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.02&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">2, gene 2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10754 BPP22])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4dkw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dkw OCA], [http://pdbe.org/4dkw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4dkw RCSB], [http://www.ebi.ac.uk/pdbsum/4dkw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4dkw ProSAT]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4dkw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dkw OCA], [https://pdbe.org/4dkw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4dkw RCSB], [https://www.ebi.ac.uk/pdbsum/4dkw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4dkw ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/TERL_BPP22 TERL_BPP22]] Component of the molecular motor that translocates genomic DNA in empty capsid during DNA packaging. Heterodimerizes with small terminase protein to be docked on capsid portal protein. The latter forms a ring in which genomic DNA in translocated into the capsid. May have or induce an endonuclease activity to cleave the genome concatemer after encapsidation (By similarity).
+[https://www.uniprot.org/uniprot/TERL_BPP22 TERL_BPP22] Component of the molecular motor that translocates genomic DNA in empty capsid during DNA packaging. Heterodimerizes with small terminase protein to be docked on capsid portal protein. The latter forms a ring in which genomic DNA in translocated into the capsid. May have or induce an endonuclease activity to cleave the genome concatemer after encapsidation (By similarity).
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Packaging of viral genomes into preformed procapsids requires the controlled and synchronized activity of an ATPase and a genome-processing nuclease, both located in the large (L) terminase subunit. In this paper, we have characterized the structure and regulation of bacteriophage P22 L-terminase (gp2). Limited proteolysis reveals a bipartite organization, consisting of an N-terminal ATPase core flexibly connected to a C-terminal nuclease domain. The 2.02 A crystal structure of P22 headful nuclease obtained by in drop proteolysis of full length L-terminase (FL-L-terminase) reveals a central seven-stranded beta-sheet core that harbors two magnesium ions. Modeling studies with DNA suggest the two ions are poised for two-metal ion-dependent catalysis, but the nuclease DNA-binding surface is sterically hindered by a loop-helix (L1-alpha2) motif, which is incompatible with catalysis. Accordingly, the isolated nuclease is completely inactive in vitro, while it exhibits endonucleolytic activity in the context of FL-L-terminase. Deleting the auto-inhibitory L1-alpha2 motif (or just the loop L1) restores nuclease activity to a level comparable to FL-L-terminase. Together, these results suggest that the activity of P22 headful nuclease is regulated by an intramolecular cross-talk with the N-terminal ATPase domain. This cross-talk allows for precise and controlled cleavage of DNA that is essential for genome-packaging.
-Structure of p22 headful packaging nuclease.,Roy A, Cingolani G J Biol Chem. 2012 Jun 19. PMID:22715098<ref>PMID:22715098</ref>
+==See Also==
+*[[Terminase 3D Structures|Terminase 3D Structures]]
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 4dkw" style="background-color:#fffaf0;"></div>
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Bpp22]]
+[[Category: Large Structures]]
-[[Category: Cingolani, G]]
+[[Category: Salmonella virus P22]]
-[[Category: Roy, A]]
+[[Category: Cingolani G]]
-[[Category: Dna]]
+[[Category: Roy A]]
-[[Category: Dna-packaging]]
-[[Category: Dna-packaging motor]]
-[[Category: Endonuclease]]
-[[Category: Hydrolase]]
-[[Category: Large terminase]]
-[[Category: Nuclease fold]]
-[[Category: Small terminase]]